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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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iTRAQ and PRM -based proteomics analysis for the identification of differentially abundant proteins related to male sterility in ms-7 mutant tomato (Solanum lycoperscium) plants. J Proteomics 2022; 261:104557. [DOI: 10.1016/j.jprot.2022.104557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/20/2022]
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3
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Lin Y, Huang R, Sun X, Yu X, Xiao Y, Wang L, Hu W, Zhong T. The p-Anisaldehyde/β-cyclodextrin inclusion complexes as fumigation agent for control of postharvest decay and quality of strawberry. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Oligosaccharide is a promising natural preservative for improving postharvest preservation of fruit: A review. Food Chem 2020; 341:128178. [PMID: 33022576 DOI: 10.1016/j.foodchem.2020.128178] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022]
Abstract
Lack of proper postharvest management of fruits causes huge economic loss, increase poverty, hunger and malnutrition. To reduce postharvest losses, globally different postharvest technologies and synthetic chemical treatments were widely used, but some of them are reported to enhance the risk for human health and environment. Recently, oligosaccharides have attractedmuch attention because of their numerous health benefits, and potential applications in agriculture. Many previous reports demonstrated that oligosaccharides treatment improves the postharvest preservation of fruits and extend the shelf life. Oligosaccharides postharvest treatments maintained higher non enzymatic antioxidant activity, increased antioxidant activity, regulate hormone biosynthesis and delayed cell wall degradation. In this review, we systematically summarize and discuss the recent research findings concerning the preservation effects of different oligosaccharides, and their mechanism underlying delaying ripening and senescence of fruits during postharvest storage. Moreover, we provide future research direction for the utilization of oligosaccharides to improve postharvest preservation of fruits.
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Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum). Sci Rep 2020; 10:14842. [PMID: 32908168 PMCID: PMC7481182 DOI: 10.1038/s41598-020-71828-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is an important crop for biofuel production but it also serves as host for greenbugs (Schizaphis graminum Rondani; GB). Although transcriptomic studies have been done to infer the molecular mechanisms of plant defense against GB, little is known about the effect of GB infestation on the switchgrass protein expression and phosphorylation regulation. The global response of the switchgrass cultivar Summer proteome and phosphoproteome was monitored by label-free proteomics shotgun in GB-infested and uninfested control plants at 10 days post infestation. Peptides matching a total of 3,594 proteins were identified and 429 were differentially expressed proteins in GB-infested plants relative to uninfested control plants. Among these, 291 and 138 were up and downregulated by GB infestation, respectively. Phosphoproteome analysis identified 310 differentially phosphorylated proteins (DP) from 350 phosphopeptides with a total of 399 phosphorylated sites. These phosphopeptides had more serine phosphorylated residues (79%), compared to threonine phosphorylated sites (21%). Overall, KEGG pathway analysis revealed that GB feeding led to the enriched accumulation of proteins important for biosynthesis of plant defense secondary metabolites and repressed the accumulation of proteins involved in photosynthesis. Interestingly, defense modulators such as terpene synthase, papain-like cysteine protease, serine carboxypeptidase, and lipoxygenase2 were upregulated at the proteome level, corroborating previously published transcriptomic data.
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Wang B, Li N, Wang J, Huang S, Tang Y, Yang S, Yang T, Wang Q, Yu Q, Gao J. iTRAQ-Based Proteomics Reveals that the Tomato ms10 35 Gene Causes Male Sterility through Compromising Fat Acid Metabolism. Proteomics 2020; 20:e1900213. [PMID: 32104964 DOI: 10.1002/pmic.201900213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 02/16/2020] [Indexed: 11/11/2022]
Abstract
So far, over 50 spontaneous male sterile mutants of tomato have been described and most of them are categorized as genetic male sterility. To date, the mechanism of tomato genetic male sterility remained unclear. In this study, differential proteomic analysis is performed between genetic male sterile line (2-517), which carries the male sterility (ms1035 ) gene, and its wild-type (VF-11) using isobaric tags for relative and absolute quantification-based strategy. A total of 8272 proteins are quantified in the 2-517 and VF-11 lines at the floral bud and florescence stages. These proteins are involved in different cellular and metabolic processes, which express obvious functional tendencies toward the hydroxylation of the ω-carbon in fatty acids, the tricarboxylic acid cycle, the glycolytic, and pentose phosphate pathways. Based on the results, a protein network explaining the mechanisms of tomato genetic male sterility is proposed, finding the compromising fat acid metabolism may cause the male sterility. These results are confirmed by parallel reaction monitoring, quantitative Real-time PCR (qRT-PCR), and physiological assays. Taken together, these results provide new insights into the metabolic pathway of anther abortion induced by ms1035 and offer useful clues to identify the crucial proteins involved in genetic male sterility in tomato.
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Affiliation(s)
- Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China.,College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, P. R. China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China.,College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, P. R. China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Shaoyong Huang
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, P. R. China
| | - Yaping Tang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Shengbao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Qiang Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China.,College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, P. R. China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Jie Gao
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, P. R. China
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Osorio S, Carneiro RT, Lytovchenko A, McQuinn R, Sørensen I, Vallarino JG, Giovannoni JJ, Fernie AR, Rose JKC. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:106-118. [PMID: 31131540 PMCID: PMC6920187 DOI: 10.1111/pbi.13176] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/26/2019] [Accepted: 05/20/2019] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening is regulated co-operatively by the action of ethylene and a hierarchy of transcription factors, including RIPENING INHIBITOR (RIN) and NON-RIPENING (NOR). Mutations in these two genes have been adopted commercially to delay ripening, and accompanying textural deterioration, as a means to prolong shelf life. However, these mutations also affect desirable traits associated with colour and nutritional value, although the extent of this trade-off has not been assessed in detail. Here, we evaluated changes in tomato fruit pericarp primary metabolite and carotenoid pigment profiles, as well as the dynamics of specific associated transcripts, in the rin and nor mutants during late development and postharvest storage, as well of those of the partially ripening delayed fruit ripening (dfd) tomato genotype. These profiles were compared with those of the wild-type tomato cultivars Ailsa Craig (AC) and M82. We also evaluated the metabolic composition of M82 fruit ripened on or off the vine over a similar period. In general, the dfd mutation resulted in prolonged firmness and maintenance of quality traits without compromising key metabolites (sucrose, glucose/fructose and glucose) and sectors of intermediary metabolism, including tricarboxylic acid cycle intermediates. Our analysis also provided insights into the regulation of carotenoid formation and highlighted the importance of the polyamine, putrescine, in extending fruit shelf life. Finally, the metabolic composition analysis of M82 fruit ripened on or off the vine provided insights into the import into fruit of compounds, such as sucrose, during ripening.
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Affiliation(s)
- Sonia Osorio
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Raphael T. Carneiro
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Anna Lytovchenko
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Ryan McQuinn
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Iben Sørensen
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - José G. Vallarino
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - James J. Giovannoni
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jocelyn K. C. Rose
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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Wu X, Yan J, Wu Y, Zhang H, Mo S, Xu X, Zhou F, Ding H. Proteomic analysis by iTRAQ-PRM provides integrated insight into mechanisms of resistance in pepper to Bemisia tabaci (Gennadius). BMC PLANT BIOLOGY 2019; 19:270. [PMID: 31226939 PMCID: PMC6588876 DOI: 10.1186/s12870-019-1849-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/24/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND The Bemisia tabaci is a major leaf feeding insect pest to pepper (Capsicum annuum), causing serious damage to pepper growth and yield. It is particularly important to study the mechanism of pepper resistance to B. tabaci, and to breed and promote the varieties of pepper resistant to B. tabaci. However, very limited molecular mechanism is available about how plants perceive and defend themselves from the destructive pest. Proteome technologies have provided an idea method for studying plant physiological processes in response to B. tabaci. RESULTS Here, a highly resistant genotype and a highly susceptible genotype were exposed to B. tabaci feeding for 48 h to explore the defense mechanisms of pepper resistance to B. tabaci. The proteomic differences between both genotypes were compared using isobaric tag for relative and absolute quantification (iTRAQ). The quantitative data were validated by parallel reaction monitoring (PRM). The results showed that 37 differential abundance proteins (DAPs) were identified in the RG (resistant genotype), while 17 DAPs were identified in the SG (susceptible genotype) at 48 h after B. tabaci feeding. 77 DAPs were identified when comparing RG with SG without feeding. The DAP functions were determined for the classification of the pathways, mainly involved in redox regulation, stress response, protein metabolism, lipid metabolism and carbon metabolism. Some candidate DAPs are closely related to B. tabaci resistance such as annexin D4-like (ANN4), calreticulin-3 (CRT3), heme-binding protein 2-like (HBP1), acidic endochitinase pcht28-like (PR3) and lipoxygenase 2 (LOX2). CONCLUSIONS Taken together, this study indicates complex resistance-related events in B. tabaci interaction, provides novel insights into the molecular mechanism underlying the response of plant to B. tabaci, and identifies some candidate proteins against B. tabaci attack.
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Affiliation(s)
- Xiaoxia Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Jiaxing Yan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Yahong Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Haibo Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Shuangrong Mo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Xiaoying Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Fucai Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Haidong Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
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Lu L, Ji L, Ma Q, Yang M, Li S, Tang Q, Qiao L, Li F, Guo Q, Wang C. Depression of Fungal Polygalacturonase Activity in Solanum lycopersicum Contributes to Antagonistic Yeast-Mediated Fruit Immunity to Botrytis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3293-3304. [PMID: 30785743 DOI: 10.1021/acs.jafc.9b00031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The acquisition of susceptibility to necrotrophy over the course of ripening is one of the critical factors limiting shelf life. In this study, phytopathology and molecular biology were employed to explore the roles of pectinase in fruit susceptibility and ripening. Solanum lycopersicum fruit softened dramatically from entirely green to 50% red, which was accompanied by a continuously high expressed SlPG2 gene. The necrotrophic fungus Botrytis cinerea further activated the expression of SlPGs and SlPMEs to accelerate cell wall disassembly, while most of the polygalacturonase inhibitor proteins encoding genes expression were postponed in ripe fruit following the pathogen attack. Pectin induced the antagonistic yeast to secrete pectinolytic enzymes to increase fruit resistance against gray mold. The activities of pathogenic pectinase of B. cinerea were correspondingly depressed in the pectin-inducible yeast enzyme elicited ripe fruit. These data suggest that pectinase is a molecular target for regulation of disease resistance during fruit ripening.
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Affiliation(s)
- Laifeng Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Lifeng Ji
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Qingqing Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Mingguan Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Shuhua Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Qiong Tang
- College of Biosystems Engineering and Food Science, National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture , Zhejiang University , Hangzhou 310058 , China
| | - Liping Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Fengjuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Qingbin Guo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Changlu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Institute for New Rural Development , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
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Li L, Wu Q, Wang Y, Aghdam MS, Ban Z, Zhang X, Lu H, Li D, Yan J, Limwachiranon J, Luo Z. Systematically quantitative proteomics and metabolite profiles offer insight into fruit ripening behavior in Fragaria × ananassa. RSC Adv 2019; 9:14093-14108. [PMID: 35519301 PMCID: PMC9064045 DOI: 10.1039/c9ra00549h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/28/2019] [Indexed: 11/21/2022] Open
Abstract
Profound metabolic and proteomic changes involved in the primary and the secondary metabolism are required for the ripeness of fleshy fruit such as strawberries (Fragaria × ananassa). Here we present the quantitative proteomic profiling in parallel with metabolic and transcriptional profiling at five developmental stages of strawberry fruit ripening, and correlations between changes in representative metabolites and the abundance of related proteins were analyzed. Hierarchical clustering analysis of the quantitative proteomic profiling identified 143 proteins in strawberry fruit across five developmental stages. Meanwhile, both protein abundance and gene expression spanned a wide range of roles, such as the primary and the secondary metabolism, defense system, and response to stress stimuli. The decreased abundance of proteins contributed to the carbohydrate metabolism and the up-regulated expression of secondary biosynthetic proteins was found to be positively correlated with the accumulation of primary and secondary metabolites during strawberry development. Moreover, with the same annotations and high homology, the gene function of key genes involved in primary and secondary metabolism (FaTPI, FaPAL, FaMDH and FaME) was confirmed in Nicotiana via the transient expression assay, which provides further evidence for the role of those genes in metabolism of strawberry fruit. The results of the present study may serve as an important resource for the functional analysis of the proteome and offer new perspectives on regulation of fruit quality. Proteome and metabolite profiles of fruit ripening behavior in Fragaria × ananassa Duch. ‘Benihoppe’.![]()
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Pan J, Li Z, Wang Q, Garrell AK, Liu M, Guan Y, Zhou W, Liu W. Comparative proteomic investigation of drought responses in foxtail millet. BMC PLANT BIOLOGY 2018; 18:315. [PMID: 30497407 PMCID: PMC6267058 DOI: 10.1186/s12870-018-1533-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it's urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level. RESULTS In this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression. CONCLUSION The results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.
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Affiliation(s)
- Jiaowen Pan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | - Zhen Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | - Qingguo Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | | | - Min Liu
- Shandong Agriculture and Engineering University, Jinan, 250100 Shandong China
| | - Yanan Guan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 Shandong China
| | | | - Wei Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 Shandong China
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Zhu Z, Zhang Y, Liu J, Chen Y, Zhang X. Exploring the effects of selenium treatment on the nutritional quality of tomato fruit. Food Chem 2018; 252:9-15. [DOI: 10.1016/j.foodchem.2018.01.064] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 01/05/2018] [Accepted: 01/07/2018] [Indexed: 12/01/2022]
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13
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Marmiroli M, Mussi F, Imperiale D, Marmiroli N. Target proteins reprogrammed by As and As + Si treatments in Solanum lycopersicum L. fruit. BMC PLANT BIOLOGY 2017; 17:210. [PMID: 29157202 PMCID: PMC5696772 DOI: 10.1186/s12870-017-1168-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/10/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arsenic is an important contaminant of many arable soils worldwide, while silicon, one of the most abundant elements in the earth's crust, interacts with As in the context of plant metabolism. As toxicity results largely from its stimulation of reactive oxygen species, and it is believed that Si can mitigate this process through reduction of the level of oxidative stress. Experiments targeting the proteomic impact of exposure to As and Si have to date largely focused on analyses of root, shoot and seed of a range of mainly non-solanaceous species, thus it remains unclear whether oxidative stress is the most important manifestation of As toxicity in Solanum lycopersicum fruit which during ripening go through drastic physiological and molecular readjustments. The role of Si also needs to be re-evaluated. RESULTS A comparison was drawn between the proteomic responses to As and As + Si treatments of the fruit of two tomato cultivars (cvs. Aragon and Gladis) known to contrast for their ability to take up these elements and to translocate them into fruits. Treatments were applied at the beginning of the red ripening stage, and the fruit proteomes were captured after a 14 day period of exposure. For each cultivar, a set of differentially abundant fruit proteins (from non-treated and treated plants) were isolated by 2DGE and identified using mass spectrometry. In the fruit of cv. Aragon, the As treatment reprogrammed proteins largely involved in transcription regulation (growth- regulating factor 9-like), and cell structure (actin-51), while in the cv. Gladis, the majority of differentially expressed proteins were associated with protein ubiquitination and proteolysis (E3 ubiquitin protein, and hormones (1-aminocyclopropane 1-carboxylase). CONCLUSIONS The present experiments were intended to establish whether Si supplementation can be used to reverse the proteomic disturbance induced by the As treatment; this reprogram was only partial and more effective in the fruit of cv. Gladis than in that of cv. Aragon. Proteins responsible for the protection of the fruits' quality in the face of As-induced stress were identified. Moreover, supplementation with Si seemed to limit to a degree the accumulation of As in the tomato fruit of cv. Aragon.
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Affiliation(s)
- Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Francesca Mussi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Davide Imperiale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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14
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Liu L, Liu H, Li S, Zhang X, Zhang M, Zhu N, Dufresne CP, Chen S, Wang Q. Regulation of BZR1 in fruit ripening revealed by iTRAQ proteomics analysis. Sci Rep 2016; 6:33635. [PMID: 27680870 PMCID: PMC5041101 DOI: 10.1038/srep33635] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
Fruit ripening is a complex and genetically programmed process. Brassinosteroids (BRs) play an essential role in plant growth and development, including fruit ripening. As a central component of BR signaling, the transcription factor BZR1 is involved in fruit development in tomato. However, the transcriptional network through which BZR1 regulates fruit ripening is mostly unknown. In this study, we use isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology to explore important proteins regulated by BZR1 in two independent tomato transgenic lines over-expressing BZR1-1D at four ripening stages, identifying 411 differentially expressed proteins. These proteins were implicated in light reaction, plant hormone pathways and cell-wall-related metabolism, etc. The ‘light reaction’ metabolic pathway was identified as a markedly enhanced pathway by BZR1 during tomato fruit ripening. The protein level of a probable 2-oxoglutarate-dependent dioxygenase 2-ODD2, involved in gibberellin biosynthesis was significantly increased at all four developmental and ripening stages. The results reveal molecular links between BR signaling pathway and downstream components involved in multiple ripening-associated events during tomato fruit ripening, which will provide new insights into the molecular mechanisms underlying tomato ripening regulatory networks, and be potential in understanding BR-regulated fruit ripening.
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Affiliation(s)
- Lihong Liu
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China.,Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Haoran Liu
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China
| | - Shuo Li
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China
| | - Xin Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China
| | - Min Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China
| | - Ning Zhu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, P.R. China.,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
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15
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Fan S, Zhang D, Lei C, Chen H, Xing L, Ma J, Zhao C, Han M. Proteome Analyses Using iTRAQ Labeling Reveal Critical Mechanisms in Alternate Bearing Malus prunifolia. J Proteome Res 2016; 15:3602-3616. [DOI: 10.1021/acs.jproteome.6b00357] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Lei
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongfei Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Juanjuan Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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16
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Sun Q, Zhang N, Wang J, Cao Y, Li X, Zhang H, Zhang L, Tan DX, Guo YD. A label-free differential proteomics analysis reveals the effect of melatonin on promoting fruit ripening and anthocyanin accumulation upon postharvest in tomato. J Pineal Res 2016; 61:138-53. [PMID: 26820691 DOI: 10.1111/jpi.12315] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/11/2022]
Abstract
To better understand the function of melatonin in tomato fruit ripening and quality improvement, a label-free quantitation method was used to investigate the proteins that differ between the control (CK) and 50 μm melatonin treatment (M50) fruits. Proteomics data identified 241 proteins that were significantly influenced by melatonin. These proteins were involved in several ripening-related pathways, including cell wall metabolism, oxidative phosphorylation, carbohydrate, and fatty acid metabolism. Moreover, the application of exogenous melatonin increased eight proteins that are related to anthocyanin accumulation during fruit ripening. Additionally, the affected protein levels correlated with the corresponding gene transcript levels. Further, the total anthocyanin content from M50 increased by 52%, 48%, and 50% at 5, 8, and 13 DAT (day after melatonin treatment), respectively. The melatonin-mediated promotion of fruit ripening and quality might be due to the altered proteins involved in processes associated with ripening. In this work, we indicated that a senescence-related protein was downregulated in the M50 fruit, while a cell apoptosis inhibitor (API5) protein was upregulated. In addition, peroxidases (POD9, POD12, peroxidase p7-like) and catalase (CAT3) significantly increased in the M50 fruits. Based on the previous studies and our data, we inferred that melatonin might be positively related to fruit ripening but negatively related to fruit senescence. This research provides insights into the physiological and molecular mechanisms underlying melatonin-mediated fruit ripening as well as the anthocyanin formation process in tomato fruit at the protein concentration level, and we reveal possible candidates for regulation of anthocyanin formation during fruit ripening.
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Affiliation(s)
- Qianqian Sun
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Na Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Jinfang Wang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Yunyun Cao
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Xingsheng Li
- Shandong Huasheng Agriculture Co. Ltd, Shandong, China
| | - Haijun Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Lei Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Dun-Xian Tan
- Department of Cellular and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Yang-Dong Guo
- College of Horticultural Science, China Agricultural University, Beijing, China
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17
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Liu R, Wang Y, Qin G, Tian S. iTRAQ-based quantitative proteomic analysis reveals the role of the tonoplast in fruit senescence. J Proteomics 2016; 146:80-9. [DOI: 10.1016/j.jprot.2016.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023]
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18
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Chialva M, Zouari I, Salvioli A, Novero M, Vrebalov J, Giovannoni JJ, Bonfante P. Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening. PLANTA 2016; 244:155-165. [PMID: 27002971 DOI: 10.1007/s00425-016-2491-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Systemic responses to an arbuscular mycorrhizal fungus reveal opposite phenological patterns in two tomato ripening mutants depending whether ethylene or light reception is involved. The availability of tomato ripening mutants has revealed many aspects of the genetics behind fleshy fruit ripening, plant hormones and light signal reception. Since previous analyses revealed that arbuscular mycorrhizal symbiosis influences tomato berry ripening, we wanted to test the hypothesis that an interplay might occur between root symbiosis and fruit ripening. With this aim, we screened seven tomato mutants affected in the ripening process for their responsiveness to the arbuscular mycorrhizal fungus Funneliformis mosseae. Following their phenological responses we selected two mutants for a deeper analysis: Green ripe (Gr), deficient in fruit ethylene perception and high-pigment-1 (hp-1), displaying enhanced light signal perception throughout the plant. We investigated the putative interactions between ripening processes, mycorrhizal establishment and systemic effects using biochemical and gene expression tools. Our experiments showed that both mutants, notwithstanding a normal mycorrhizal phenotype at root level, exhibit altered arbuscule functionality. Furthermore, in contrast to wild type, mycorrhization did not lead to a higher phosphate concentration in berries of both mutants. These results suggest that the mutations considered interfere with arbuscular mycorrhiza inducing systemic changes in plant phenology and fruits metabolism. We hypothesize a cross talk mechanism between AM and ripening processes that involves genes related to ethylene and light signaling.
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Affiliation(s)
- Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Inès Zouari
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Mara Novero
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
- US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, NY, USA
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy.
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19
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Onelli E, Ghiani A, Gentili R, Serra S, Musacchi S, Citterio S. Specific Changes of Exocarp and Mesocarp Occurring during Softening Differently Affect Firmness in Melting (MF) and Non Melting Flesh (NMF) Fruits. PLoS One 2015; 10:e0145341. [PMID: 26709823 PMCID: PMC4692397 DOI: 10.1371/journal.pone.0145341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/02/2015] [Indexed: 12/24/2022] Open
Abstract
Melting (MF) and non melting flesh (NMF) peaches differ in their final texture and firmness. Their specific characteristics are achieved by softening process and directly dictate fruit shelf life and quality. Softening is influenced by various mechanisms including cell wall reorganization and water loss. In this work, the biomechanical properties of MF Spring Crest's and NMF Oro A's exocarp and mesocarp along with the amount and localization of hydroxycinnamic acids and flavonoids were investigated during fruit ripening and post-harvest. The objective was to better understand the role played by water loss and cell wall reorganization in peach softening. Results showed that in ripe Spring Crest, where both cell turgor loss and cell wall dismantling occurred, mesocarp had a little role in the fruit reaction to compression and probe penetration response was almost exclusively ascribed to the epidermis which functioned as a mechanical support to the pulp. In ripe Oro A's fruit, where cell wall disassembly did not occur and the loss of cell turgor was observed only in mesocarp, the contribution of exocarp to fruit firmness was consistent but relatively lower than that of mesocarp, suggesting that in addition to cell turgor, the integrity of cell wall played a key role in maintaining NMF fruit firmness. The analysis of phenols suggested that permeability and firmness of epidermis were associated with the presence of flavonoids and hydroxycinnamic acids.
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Affiliation(s)
- E. Onelli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy
| | - A. Ghiani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza n. 1, 20126, Milan, Italy
| | - R. Gentili
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza n. 1, 20126, Milan, Italy
| | - S. Serra
- Department of Horticulture, Washington State University, TFREC, Wenatchee, 98801, WA, United States of America
| | - S. Musacchi
- Department of Horticulture, Washington State University, TFREC, Wenatchee, 98801, WA, United States of America
| | - S. Citterio
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza n. 1, 20126, Milan, Italy
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20
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Song F, Qi D, Liu X, Kong X, Gao Y, Zhou Z, Wu Q. Proteomic analysis of symbiotic proteins of Glomus mosseae and Amorpha fruticosa. Sci Rep 2015; 5:18031. [PMID: 26658758 PMCID: PMC4674871 DOI: 10.1038/srep18031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/10/2015] [Indexed: 11/25/2022] Open
Abstract
Arbuscular mycorrhiza fungi (AMF) can colonize the roots of Amorpha fruticosa, a perennial leguminous woody shrub, and form arbuscular mycorrhiza (AM). AMF have significant promoting effects on A. fruticosa growth as the intensity of fungal colonization increases. Taking AMF-A. fruticosa symbionts as the experimental material, gel-free isobaric tags for relative and absolute quantification (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to investigate the expression of A. fruticosa mycorrhizal proteins at the maturation stage. A total of 3,473 proteins were identified, of which 77 showed dramatic changes in their root expression levels; 33 increased, and 44 decreased. We also found nine AMF proteins that were expressed with AMF treatment. The 77 proteins were classified according to function. Plant proteins were assigned into 11 categories: metabolism-related (32%), protein folding and degradation-related (22%), energy-related (10%), protein synthesis-related (8%), stress and defense-related (24%), transcription-related (6%), membrane and transport-related (4%), cellular structure-related (2.5%), signaling transduction-related (11%) and unknown proteins (5%). The results of the study provide a foundation for further investigation of the metabolic characteristics and molecular mechanisms of AM.
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Affiliation(s)
- Fuqiang Song
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Dandan Qi
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Xuan Liu
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Xiangshi Kong
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Yang Gao
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Zixin Zhou
- Heilongjiang University, Harbin, Heilongjiang, China
| | - Qi Wu
- Heilongjiang University, Harbin, Heilongjiang, China
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21
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Li JM, Huang XS, Li LT, Zheng DM, Xue C, Zhang SL, Wu J. Proteome analysis of pear reveals key genes associated with fruit development and quality. PLANTA 2015; 241:1363-1379. [PMID: 25682102 DOI: 10.1007/s00425-015-2263-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Comparative and association analyses of the proteome and transcriptome for pear fruit development were conducted for the first time in this study. Pear fruit development involves complex physiological and biochemical processes, but there is still little knowledge available at proteomic and transcriptomic levels, which would be helpful for understanding the molecular mechanisms of fruit development and quality in pear. In our study, three important stages, including early development (S4-22), middle development (S6-27), and near ripening (S8-30), were investigated in 'Dangshansuli' by isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology, identifying a total of 1,810 proteins during pear fruit development. The association analysis of proteins and transcript expression revealed 1,724, 1,722, and 1,718 associated proteins identified in stages S4-22, S6-27, and S8-30, respectively. A total of 237, 318, and 425 unique proteins were identified as differentially expressed during S4-22 vs S6-27, S6-27 vs S8-30, S4-22 vs S8-30, respectively, and the corresponding correlation coefficients of the overall differentially expressed proteins and transcripts data were 0.6336, 0.4113, and 0.7049. The phenylpropanoid biosynthesis pathway, which is related to lignin formation of pear fruit, was identified as a significantly enriched pathway during early stages of fruit development. Finally, a total of 35 important differentially expressed proteins related to fruit quality were identified, including three proteins related to sugar formation, seven proteins related to aroma synthesis, and sixteen proteins related to the formation of lignin. In addition, qRT-PCR verification provided further evidence to support differentially expressed gene selection. This study is the first to reveal protein and associated mRNA variations in pear during fruit development and quality conformation, and identify key genes and proteins helpful for future functional genomics studies, and provides gene resources for improvement of pear quality.
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Affiliation(s)
- Jia Ming Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
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22
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Gapper NE, Giovannoni JJ, Watkins CB. Understanding development and ripening of fruit crops in an 'omics' era. HORTICULTURE RESEARCH 2014; 1:14034. [PMID: 26504543 PMCID: PMC4596339 DOI: 10.1038/hortres.2014.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 05/17/2023]
Abstract
Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.
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Affiliation(s)
- Nigel E Gapper
- Department of Horticulture, Cornell University, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- mailto:
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- Plant, Soil, and Nutrition Laboratory, US Department of Agriculture/Agriculture Research Service, Ithaca, NY 14853, USA
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